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Добірка наукової літератури з теми "DnaB helicase"

Автор: Grafiati

Опубліковано: 4 березня 2024

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Статті в журналах з теми "DnaB helicase"

Titok, Marina, Catherine Suski, Bérengère Dalmais, S. Dusko Ehrlich, and Laurent Jannière. "The replicative polymerases PolC and DnaE are required for theta replication of the Bacillus subtilis plasmid pBS72." Microbiology 152, no. 5 (May 1, 2006): 1471–78. http://dx.doi.org/10.1099/mic.0.28693-0.

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Plasmids are the tools of choice for studying bacterial functions involved in DNA maintenance. Here a genetic study on the replication of a novel, low-copy-number, Bacillus subtilis plasmid, pBS72, is reported. The results show that two plasmid elements, the initiator protein RepA and an iteron-containing origin, and at least nine host-encoded replication proteins, the primosomal proteins DnaB, DnaC, DnaD, DnaG and DnaI, the DNA polymerases DnaE and PolC, and the polymerase cofactors DnaN and DnaX, are required for pBS72 replication. On the contrary, the cellular initiators DnaA and PriA, the helicase PcrA and DNA polymerase I are dispensable. From this, it is inferred that pBS72 replication is of the theta type and is initiated by an original mechanism. Indirect evidence suggests that during this process the DnaC helicase might be delivered to the plasmid origin by the weakly active DnaD pathway stimulated by a predicted interaction between DnaC and a domain of RepA homologous to the major DnaC-binding domain of the cellular initiator DnaA. The plasmid pBS72 replication fork appears to require the same functions as the bacterial chromosome and the unrelated plasmid pAMβ1. Most importantly, this replication machinery contains the two type C polymerases, PolC and DnaE. As the mechanism of initiation of the three genomes is substantially different, this suggests that both type C polymerases might be required in any Cairns replication in B. subtilis and presumably in other bacteria encoding PolC and DnaE.

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Hayashi, Chihiro, Erika Miyazaki, Shogo Ozaki, Yoshito Abe, and Tsutomu Katayama. "DnaB helicase is recruited to the replication initiation complex via binding of DnaA domain I to the lateral surface of the DnaB N-terminal domain." Journal of Biological Chemistry 295, no. 32 (June 15, 2020): 11131–43. http://dx.doi.org/10.1074/jbc.ra120.014235.

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The DNA replication protein DnaA in Escherichia coli constructs higher-order complexes on the origin, oriC, to unwind this region. DnaB helicase is loaded onto unwound oriC via interactions with the DnaC loader and the DnaA complex. The DnaB–DnaC complex is recruited to the DnaA complex via stable binding of DnaB to DnaA domain I. The DnaB–DnaC complex is then directed to unwound oriC via a weak interaction between DnaB and DnaA domain III. Previously, we showed that Phe46 in DnaA domain I binds to DnaB. Here, we searched for the DnaA domain I–binding site in DnaB. The DnaB L160A variant was impaired in binding to DnaA complex on oriC but retained its DnaC-binding and helicase activities. DnaC binding moderately stimulated DnaA binding of DnaB L160A, and loading of DnaB L160A onto oriC was consistently and moderately inhibited. In a helicase assay with partly single-stranded DNA bearing a DnaA-binding site, DnaA stimulated DnaB loading, which was strongly inhibited in DnaB L160A even in the presence of DnaC. DnaB L160A was functionally impaired in vivo. On the basis of these findings, we propose that DnaB Leu160 interacts with DnaA domain I Phe46. DnaB Leu160 is exposed on the lateral surface of the N-terminal domain, which can explain unobstructed interactions of DnaA domain I–bound DnaB with DnaC, DnaG primase, and DnaA domain III. We propose a probable structure for the DnaA–DnaB–DnaC complex, which could be relevant to the process of DnaB loading onto oriC.

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Bazin, Alexandre, Mickaël Cherrier, and Laurent Terradot. "Structural insights into DNA replication initiation in Helicobacter pylori." Acta Crystallographica Section A Foundations and Advances 70, a1 (August 5, 2014): C1632. http://dx.doi.org/10.1107/s2053273314083673.

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In Gram-negative bacteria, opening of DNA double strand during replication is performed by the replicative helicase DnaB. This protein allows for replication fork elongation by unwinding DNA and interacting with DnaG primase. DnaB is composed of two domains: an N-terminal domain (NTD) and a C-terminal domain (CTD) connected by a flexible linker. The protein forms two-tiered hexamers composed of a NTD-ring and a CTD-ring. In Escherichia coli, the initiator protein DnaA binds to the origin of replication oriC and induces the opening of a AT-rich region. The replicative helicase DnaB is then loaded onto single stranded DNA by interacting with DnaA and with the AAA+ helicase loader DnaC. However, AAA+ loaders are absent in 80% of the bacterial genome, raising the question of how helicases are loaded in these bacteria [1]. In the genome of human pathogen Helicobacter pylori, no AAA+ loader has been identified. Moreover H. pylori DnaB (HpDnaB) has the ability to support replication of an otherwise unviable E. coli strain that bears a defective copy of DnaC by complementation [2]. In order to better understand the properties of HpDnaB we have first shown that HpDnaB forms double hexamers by negative stain electron microscopy [3]. Then, we have then solved the crystal structure of HpDnaB at a resolution of 6.7Å by X-ray crystallography with Rfree/Rfactor of 0.29/0.25. The structure reveals that the protein adopts a new dodecameric arrangement generated by crystallographic three fold symmetry. When compared to hexameric DnaBs, the hexamer of HpDnaB displays an original combination of NTD-ring and CTD-ring symmetries, intermediate between apo and ADP-bound structure. Biochemistry studies of HpDnaB interaction with HpDnaG-CTD and ssDNA provides mechanistic insights into the initial steps of DNA replication in H. pylori. Our results offer an alternative solution of helicase loading and DNA replication initiation in H. pylori and possibly other bacteria that do not employ helicase loaders.

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Huang, Yen-Hua, and Cheng-Yang Huang. "Structural Insight into the DNA-Binding Mode of the Primosomal Proteins PriA, PriB, and DnaT." BioMed Research International 2014 (2014): 1–14. http://dx.doi.org/10.1155/2014/195162.

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Replication restart primosome is a complex dynamic system that is essential for bacterial survival. This system uses various proteins to reinitiate chromosomal DNA replication to maintain genetic integrity after DNA damage. The replication restart primosome inEscherichia coliis composed of PriA helicase, PriB, PriC, DnaT, DnaC, DnaB helicase, and DnaG primase. The assembly of the protein complexes within the forked DNA responsible for reloading the replicative DnaB helicase anywhere on the chromosome for genome duplication requires the coordination of transient biomolecular interactions. Over the last decade, investigations on the structure and mechanism of these nucleoproteins have provided considerable insight into primosome assembly. In this review, we summarize and discuss our current knowledge and recent advances on the DNA-binding mode of the primosomal proteins PriA, PriB, and DnaT.

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Sharma, Dhakaram Pangeni, Ramachandran Vijayan, Syed Arif Abdul Rehman, and Samudrala Gourinath. "Structural insights into the interaction of helicase and primase in Mycobacterium tuberculosis." Biochemical Journal 475, no. 21 (November 15, 2018): 3493–509. http://dx.doi.org/10.1042/bcj20180673.

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The helicase–primase interaction is an essential event in DNA replication and is mediated by the highly variable C-terminal domain of primase (DnaG) and N-terminal domain of helicase (DnaB). To understand the functional conservation despite the low sequence homology of the DnaB-binding domains of DnaGs of eubacteria, we determined the crystal structure of the helicase-binding domain of DnaG from Mycobacterium tuberculosis (MtDnaG-CTD) and did so to a resolution of 1.58 Å. We observed the overall structure of MtDnaG-CTD to consist of two subdomains, the N-terminal globular region (GR) and the C-terminal helical hairpin region (HHR), connected by a small loop. Despite differences in some of its helices, the globular region was found to have broadly similar arrangements across the species, whereas the helical hairpins showed different orientations. To gain insights into the crucial helicase–primase interaction in M. tuberculosis, a complex was modeled using the MtDnaG-CTD and MtDnaB-NTD crystal structures. Two nonconserved hydrophobic residues (Ile605 and Phe615) of MtDnaG were identified as potential key residues interacting with MtDnaB. Biosensor-binding studies showed a significant decrease in the binding affinity of MtDnaB-NTD with the Ile605Ala mutant of MtDnaG-CTD compared with native MtDnaG-CTD. The loop, connecting the two helices of the HHR, was concluded to be largely responsible for the stability of the DnaB–DnaG complex. Also, MtDnaB-NTD showed micromolar affinity with DnaG-CTDs from Escherichia coli and Helicobacter pylori and unstable binding with DnaG-CTD from Vibrio cholerae. The interacting domains of both DnaG and DnaB demonstrate the species-specific evolution of the replication initiation system.

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Nagata, Koji, Akitoshi Okada, Jun Ohtsuka, Takatoshi Ohkuri, Yusuke Akama, Yukari Sakiyama, Erika Miyazaki, et al. "Crystal structure of the complex of the interaction domains of Escherichia coli DnaB helicase and DnaC helicase loader: structural basis implying a distortion-accumulation mechanism for the DnaB ring opening caused by DnaC binding." Journal of Biochemistry 167, no. 1 (October 30, 2019): 1–14. http://dx.doi.org/10.1093/jb/mvz087.

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Abstract Loading the bacterial replicative helicase DnaB onto DNA requires a specific loader protein, DnaC/DnaI, which creates the loading-competent state by opening the DnaB hexameric ring. To understand the molecular mechanism by which DnaC/DnaI opens the DnaB ring, we solved 3.1-Å co-crystal structure of the interaction domains of Escherichia coli DnaB–DnaC. The structure reveals that one N-terminal domain (NTD) of DnaC interacts with both the linker helix of a DnaB molecule and the C-terminal domain (CTD) of the adjacent DnaB molecule by forming a three α-helix bundle, which fixes the relative orientation of the two adjacent DnaB CTDs. The importance of the intermolecular interface in the crystal structure was supported by the mutational data of DnaB and DnaC. Based on the crystal structure and other available information on DnaB–DnaC structures, we constructed a molecular model of the hexameric DnaB CTDs bound by six DnaC NTDs. This model suggested that the binding of a DnaC would cause a distortion in the hexameric ring of DnaB. This distortion of the DnaB ring might accumulate by the binding of up to six DnaC molecules, resulting in the DnaB ring to open.

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Donate, L. E., M. Bárcena, O. Llorca, N. Dixon, and J. M. Carazo. "Quaternary Polymorphism in Helicases and the DnaB.DnaC Complex." Microscopy and Microanalysis 6, S2 (August 2000): 272–73. http://dx.doi.org/10.1017/s1431927600033857.

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Strand separation in double stranded DNA is achieved in vivo by a class of enzymes called helicases in a process fuelled by hydrolysis of nucleoside triphosphates. DnaB is the major replicative helicase in E.coli. For chromosomal replication to initiate, DnaB needs to interact with a partner protein, namely DnaC, which after properly loading DnaB onto the DNA template at the origin of replication is subsequently released from the complex. DnaB turns to be functionally active as a helicase only after DnaC has been released from the complex. The native DnaB is a homohexamer of molecular weight 318 kD. In the presence of ATP and Mg2+, the hexameric DnaB has been shown to form a complex with six molecules of DnaC (total molecular weight of the complex: 480 kD).The reconstructed 3D volume of the DnaB hexamer obtained from frozen-hydrated specimens showed the DnaB oligomer as a particle possessing three-fold rather than six-fold symmetry, despite DnaB being made up by six identical subunits.

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Saveson, Catherine J., and Susan T. Lovett. "Enhanced Deletion Formation by Aberrant DNA Replication in Escherichia coli." Genetics 146, no. 2 (June 1, 1997): 457–70. http://dx.doi.org/10.1093/genetics/146.2.457.

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Repeated genes and sequences are prone to genetic rearrangements including deletions. We have investigated deletion formation in Escherichia coli strains mutant for various replication functions. Deletion was selected between 787 base pair tandem repeats carried either on a ColE1-derived plasmid or on the E. coli chromosome. Only mutations in functions associated with DNA Polymerase III elevated deletion rates in our assays. Especially large increases were observed in strains mutant in dnaQ the ϵ editing subunit of Pol III, and dnuB, the replication fork helicase. Mutations in several other functions also altered deletion formation: the α polymerase (dnaE), the γ clamp loader complex (holC, dnaX), and the β clamp (dnaN) subunits of Pol III and the primosomal proteins, dnaC and priA. Aberrant replication stimulated deletions through several pathways. Whereas the elevation in dnaB strains was mostly recA- and lexA-dependent, that in dnaQ strains was mostly recA- and lexA-independent. Deletion product analysis suggested that slipped mispairing, producing monomeric replicon products, may be preferentially increased in a dnaQ mutant and sister-strand exchange, producing dimeric replicon products, may be elevated in dnaE mutants. We conclude that aberrant Polymerase III replication can stimulate deletion events through several mechanisms of deletion and via both recA-dependent and independent pathways.

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Odegrip, Richard, Stephan Schoen, Elisabeth Haggård-Ljungquist, Kyusung Park, and Dhruba K. Chattoraj. "The Interaction of Bacteriophage P2 B Protein with Escherichia coli DnaB Helicase." Journal of Virology 74, no. 9 (May 1, 2000): 4057–63. http://dx.doi.org/10.1128/jvi.74.9.4057-4063.2000.

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ABSTRACT Bacteriophage P2 requires several host proteins for lytic replication, including helicase DnaB but not the helicase loader, DnaC. Some genetic studies have suggested that the loading is done by a phage-encoded protein, P2 B. However, a P2 minichromosome containing only the P2 initiator gene A and a marker gene can be established as a plasmid without requiring the P2 B gene. Here we demonstrate that P2 B associates with DnaB. This was done by using the yeast two-hybrid system in vivo and was confirmed in vitro, where 35S-labeled P2 B bound specifically to DnaB adsorbed to Q Sepharose beads and monoclonal antibodies directed against the His-tagged P2 B protein were shown to coprecipitate the DnaB protein. Finally, P2 B was shown to stabilize the opening of a reporter origin, a reaction that is facilitated by the inactivation of DnaB. In this respect, P2 B was comparable to λ P protein, which is known to be capable of binding and inactivating the helicase while acting as a helicase loader. Even though P2 B has little similarity to other known or predicted helicase loaders, we suggest that P2 B is required for efficient loading of DnaB and that this role, although dispensable for P2 plasmid replication, becomes essential for P2 lytic replication.

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Spinks, Richard R., Lisanne M. Spenkelink, Sarah A. Stratmann, Zhi-Qiang Xu, N. Patrick J. Stamford, Susan E. Brown, Nicholas E. Dixon, Slobodan Jergic, and Antoine M. van Oijen. "DnaB helicase dynamics in bacterial DNA replication resolved by single-molecule studies." Nucleic Acids Research 49, no. 12 (June 17, 2021): 6804–16. http://dx.doi.org/10.1093/nar/gkab493.

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Abstract In Escherichia coli, the DnaB helicase forms the basis for the assembly of the DNA replication complex. The stability of DnaB at the replication fork is likely important for successful replication initiation and progression. Single-molecule experiments have significantly changed the classical model of highly stable replication machines by showing that components exchange with free molecules from the environment. However, due to technical limitations, accurate assessments of DnaB stability in the context of replication are lacking. Using in vitro fluorescence single-molecule imaging, we visualise DnaB loaded on forked DNA templates. That these helicases are highly stable at replication forks, indicated by their observed dwell time of ∼30 min. Addition of the remaining replication factors results in a single DnaB helicase integrated as part of an active replisome. In contrast to the dynamic behaviour of other replisome components, DnaB is maintained within the replisome for the entirety of the replication process. Interestingly, we observe a transient interaction of additional helicases with the replication fork. This interaction is dependent on the τ subunit of the clamp-loader complex. Collectively, our single-molecule observations solidify the role of the DnaB helicase as the stable anchor of the replisome, but also reveal its capacity for dynamic interactions.

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Дисертації з теми "DnaB helicase"

Atkinson, John David. "Regulation of the E. coli Replicative Helicase DnaB by the Helicase Loader DnaC." Thesis, University of Glasgow, 2007. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.485809.

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The helicase proteins directly ~esponsible for unwinding chromosomal DNA during DNA replication in bacteria, archaea and eukaryotes adopt a ring-shaped conformation for rapid displacement ofthe parental DNA duplex. As the DNA substrate is engulfed by the helicase during t~slocation, accessory proteins are required for placement ofthe helicase onto the DNA substrate either by breaking the ringed complex, thus allowing DNA to pass into the central channel, or by assembling the helicase around the DNA. In E. coli, the replicative helicase is a hexameric complex of six DnaB monomers, whilst the accessory loading partner is DnaC. Six DnaCmonomers associate with DnaB6 to assist in the loading ofthe helicase onto the DNA substrate. However, once present on the DNA, the presence ofDnaC on the DNA-bound helicase is thought to prevent the initiation of translocation. Only when DnaC has dissociated from DnaB6 will the helicase be permitted to commence unwinding ofthe duplex DNA. ,. Using in vitro enzymatic assays to identify the helicase activity ofDnaB on partial duplex DNA substrates, I have shown that when the concentration ofDnaC exceeds that ofDnaB, translocation and strand displacement by the helicase is not hindered when only one DNA strand is incorporated. When the helicase translocates over two DNA strands, however, movement is terminated via interaction with DnaC. More specifically, DnaB translocation is halted when DnaC is coupled with ATP, while interaction with ADP permits continued helicase movement. In vivo, the presence of DnaC within the DNA replication machinery complex could prove advantageous to the cell, as chromosomal duplication will only be permitted at bonefide replication forks. Keywords: DNA replication, helicase, DnaB, DnaC

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Arribas, Bosacoma Raquel. "Resolució de l'estructura tridimensional de l'helicasa hexamètrica DnaB." Doctoral thesis, Universitat de Girona, 2009. http://hdl.handle.net/10803/7639.

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Es presenta el model atòmic a 4.5 Å de DnaB, la principal helicasa replicativa bacteriana, d'Aquifex aeolicus. És un anell hexamèric de 100 Å d'amplada i 80 Å d'alçada amb dues capes de simetria diferenciada, la dels dominis N-terminals en C3 i la dels C-terminals propera a C6. El diàmetre central és de 25 Å al llarg d'ambdues capes, principal diferència amb les estructures prèvies, on era 25 Å més estret a la capa N-terminal. L'estretament s'origina pel trencament d'una de les dues superfícies d'interacció entre monòmers N-terminals, cosa que augmenta la flexibilitat del subdomini implicat. Només l'ssDNA pot atravessar l'anell, quan a les estructures prèvies hi podia passar tant ssDNA com dsDNA. L'estructura aquí presentada és més propera a la conformació funcional de DnaB durant la realització de l'activitat helicasa, mentre que les anteriors correspondrien a la forma inactiva o a la conformació capaç de translocar-se sobre dsDNA.
DnaB is the main replicative helicase in bacteria. An atomic model for the DnaB from Aquifex aeolicus at a 4.5 Å resolution is presented. It´s a ring-shaped homohexamer (100 Å width and 80 Å hight) with two simmetry layers, a C3 N-terminal layer and an almost C6 C-terminal one. The diameter of the central channel is 25 Å along both layers, being the main diference with the previously solved structures, which were 25 Å smaller along the N-terminal layer. This is due to one of the previous interacting surphaces being lost in the current structure, thus enabling a higher felxibility of the subdomain involved. Only ssDNA can pass trhough the ring, while both ssDNA and dsDNA could in the previous structures. So, the present structure is closer to the functional conformation, while the previous ones would correspond to the inactive form or the conformation that is only able to translocate along dsDNA.

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Weigelt, Johan. "Development of new NMR techniques and the structure of the N-terminal domain of Escherichia coli DnaB helicase /." Stockholm, 1999. http://diss.kib.ki.se/1999/91-628-3414-2.

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McRobbie, Anne-Marie M. "Splitting, joining and cutting : mechanistic studies of enzymes that manipulate DNA." Thesis, University of St Andrews, 2010. http://hdl.handle.net/10023/951.

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DNA is a reactive and dynamic molecule that is continually damaged by both exogenous and endogenous agents. Various DNA repair pathways have evolved to ensure the faithful replication of the genome. One such pathway, nucleotide excision repair (NER), involves the concerted action of several proteins to repair helix-distorting lesions that arise following exposure to UV light. Mutation of NER proteins is associated with several genetic diseases, including xeroderma pigmentosum that can arise upon mutation of the DNA helicase, XPD. The consequences of introducing human mutations into the gene encoding XPD from Sulfolobus acidocaldarius (SacXPD) were investigated to shed light on the molecular basis of XPD-related diseases. XPD is a 5’-3’ DNA helicase that requires an iron-sulphur (FeS) cluster for activity (Rudolf et al., 2006). Several proteins related to SacXPD, including human XPD, human FancJ and E. coli DinG, also rely on an FeS cluster for DNA unwinding (Rudolf et al., 2006; Pugh et al., 2008; Ren et al., 2009). Sequence analysis of the homologous protein, DinG, from Staphylococcus aureus (SarDinG) suggests that this protein does not encode a FeS cluster. In addition, SarDinG comprises an N-terminal extension with homology to the epsilon domain of polymerase III from E. coli. This thesis describes the purification and characterisation of SarDinG. During replication, DNA lesions or other ‘roadblocks’, such as DNA-bound proteins, can lead to replication fork stalling or collapse. To maintain genomic integrity, the fork must be restored and replication restarted. In archaea, the DNA helicase Hel308 is thought to play a role in this process by removing the lagging strands of stalled forks, thereby promoting fork repair by homologous recombination. Potential roles of Hel308 during replication fork repair are discussed in this thesis. The mechanism by which Hel308 moves along and unwinds DNA was also investigated using a combined structural and biophysical approach. The exchange of DNA between homologous strands, catalysed by a RecA family protein (RecA in bacteria, RAD51 in eukaryotes, and RadA in archaea), defines homologous recombination. While bacteria encode a single RecA protein, both eukaryotes and archaea encode multiple paralogues that have implications in the regulation of RAD51 and RadA activity, respectively. This thesis describes the purification and characterisation of one of the RadA paralogues (Sso2452) in archaea.

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Song, Daqing. "Homologous Strand Exchange and DNA Helicase Activities in Plant Mitochondria." Diss., CLICK HERE for online access, 2005. http://contentdm.lib.byu.edu/ETD/image/etd931.pdf.

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Leah, Labib. "Helicase Purification for DNA Sequencing." Thesis, Université d'Ottawa / University of Ottawa, 2014. http://hdl.handle.net/10393/31341.

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BACKGROUND: A method to increase accuracy and ease-of-use, while decreasing time and cost in deoxyribonucleic acid (DNA) sequence identification, is sought after. Helicase, which unwinds DNA, and avidin, which strongly attracts biotin for potential attraction of biotinylated DNA segments, were investigated for use in a novel DNA sequencing method. AIM: This study aimed to (1) purify bacteriophage T7 gene product 4 helicase and helicase-avidin fusion protein in a bacterial host and (2) characterize their functionality. METHODS: Helicase and helicase-avidin were cloned for purification from bacteria. Helicase-avidin was solubilised via urea denaturation/renaturation. DNA and biotin binding were assessed using Electrophoretic Mobility Shift Assays and biotinylated resins, respectively. RESULTS: (1) Helicase and helicase-avidin proteins were successfully purified. (2) Helicase protein was able to bind DNA and avidin protein strongly bound biotin. CONCLUSION: Helicase and helicase-avidin can be purified in a functional form from a bacterial host, thus supporting further investigation for DNA sequencing purposes.

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Rudolf, Jana. "Characterisation of XPD from Sulfolobus acidocaldarius : an iron-sulphur cluster containing DNA repair helicase." Thesis, St Andrews, 2007. http://hdl.handle.net/10023/159.

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Korhonen, Jenny. "Functional and structural characterization of the human mitochondrial helicase /." Stockholm : Karolinska institutet, 2007. http://diss.kib.ki.se/2007/978-91-7357-102-2/.

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Johnson, Vinu. "Structural and Biophysical Studies of Single-Stranded DNA Binding Proteins and dnaB Helicases, Proteins Involved in DNA Replication and Repair." University of Toledo / OhioLINK, 2007. http://rave.ohiolink.edu/etdc/view?acc_num=toledo1198939056.

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Tasleem, Arsala. "Helicase Attachment to Carbon Nanotubes for DNA Sensor." Thesis, Université d'Ottawa / University of Ottawa, 2018. http://hdl.handle.net/10393/37392.

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Purpose: Current DNA detection techniques require complicated procedures, specialized training, expensive equipment, invasive samples and significant amount of sample collection and processing time. The purpose of this research was to develop a rapid, accurate, non-invasive and electronic method of DNA sensing that harnesses natural unwinding properties of DNA helicase by attaching it to Carbon Nanotubes. Methods: a. A literature review on methods of attaching proteins to carbon nanotubes was conducted b. A design of the biosensor was developed based on previously reported attachment methods for other proteins c. A part of the sensor was developed by attaching DNA helicase to carbon nanotubes d. The result was tested for preservation of helicase functionality and carbon nanotube electronic structure integrity Results: a. Helicase was successfully attached to carbon nanotubes b. Helicase was found to retain its NTP hydrolysis function, DNA binding and DNA unwinding ability upon attachment c. Carbon nanotube electronic structure and function was not compromised upon attachment Conclusions: Non-specific attachment of helicase to carbon nanotubes preserves enzyme structure and function, allowing rapid DNA unwinding at an in vitro rate comparable to DNA helicase.

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Книги з теми "DnaB helicase"

D, Knudsen Walter, and Bruns Sam S, eds. Bacterial DNA, DNA polymerase, and DNA helicases. Hauppauge, NY: Nova Science, 2009.

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Spies, Maria, ed. DNA Helicases and DNA Motor Proteins. New York, NY: Springer New York, 2013. http://dx.doi.org/10.1007/978-1-4614-5037-5.

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Helicases: Methods and protocols. New York, N.Y: Humana Press, 2010.

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Lombard, David B. Biochemistry and genetics of recq-helicases. Boston, MA: Kluwer Academic Publishers, 2001.

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Lombard, David B. Biochemistry and genetics of recq-helicases. Boston, MA: Kluwer Academic Publishers, 2001.

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N, Potaman Vladimir, ed. Triple-helical nucleic acids. New York: Spinger, 1996.

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Spies, Maria. DNA Helicases and DNA Motor Proteins. Springer New York, 2014.

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Spies, Maria. DNA Helicases and DNA Motor Proteins. Springer London, Limited, 2012.

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Abdelhaleem, Mohamed M. Helicases: Methods and Protocols. Humana Press, 2012.

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Lombard, David B. Biochemistry and Genetics of RecQ-Helicases. Springer, 2012.

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Частини книг з теми "DnaB helicase"

Schomburg, Dietmar, and Ida Schomburg. "DNA helicase 3.6.4.12." In Class 3.4–6 Hydrolases, Lyases, Isomerases, Ligases, 312–53. Berlin, Heidelberg: Springer Berlin Heidelberg, 2013. http://dx.doi.org/10.1007/978-3-642-36260-6_24.

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Kokubo, Tetsuro. "Chromodomain Helicase DNA Binding (CHD)." In Encyclopedia of Systems Biology, 402–4. New York, NY: Springer New York, 2013. http://dx.doi.org/10.1007/978-1-4419-9863-7_1619.

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Klein, Hannah L. "DNA helicases in recombination." In Molecular Genetics of Recombination, 135–67. Berlin, Heidelberg: Springer Berlin Heidelberg, 2007. http://dx.doi.org/10.1007/978-3-540-71021-9_5.

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Jovin, Thomas M. "The Origin of Left-Handed Poly[d(G-C)]." In Methods in Molecular Biology, 1–32. New York, NY: Springer US, 2023. http://dx.doi.org/10.1007/978-1-0716-3084-6_1.

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AbstractThe discovery of a reversible transition in the helical sense of a double-helical DNA was initiated by the first synthesis in 1967 of the alternating sequence poly[d(G-C)]. In 1968, exposure to high salt concentration led to a cooperative isomerization of the double helix manifested by an inversion in the CD spectrum in the 240–310 nm range and in an altered absorption spectrum. The tentative interpretation, reported in 1970 and then in detailed form in a 1972 publication by Pohl and Jovin, was that the conventional right-handed B-DNA structure (R) of poly[d(G-C)] transforms at high salt concentration into a novel, alternative left-handed (L) conformation. The historical course of this development and its aftermath, culminating in the first crystal structure of left-handed Z-DNA in 1979, is described in detail. The research conducted by Pohl and Jovin after 1979 is summarized, ending with an assessment of “unfinished business”: condensed Z*-DNA; topoisomerase IIα (TOP2A) as an allosteric ZBP (Z-DNA-binding protein); B–Z transitions of phosphorothioate-modified DNAs; and parallel-stranded poly[d(G-A)], a double helix with high stability under physiological conditions and potentially also left-handed.

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Zhang, Suisheng, and Frank Grosse. "Molecular Characterization of Nuclear DNA Helicase II (RNA Helicase A)." In Methods in Molecular Biology, 291–302. Totowa, NJ: Humana Press, 2009. http://dx.doi.org/10.1007/978-1-60327-355-8_21.

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Lu, Linchao, Weidong Jin, Hao Liu, and Lisa L. Wang. "RECQ DNA Helicases and Osteosarcoma." In Advances in Experimental Medicine and Biology, 129–45. Cham: Springer International Publishing, 2014. http://dx.doi.org/10.1007/978-3-319-04843-7_7.

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Lu, Linchao, Weidong Jin, and Lisa L. Wang. "RECQ DNA Helicases and Osteosarcoma." In Current Advances in the Science of Osteosarcoma, 37–54. Cham: Springer International Publishing, 2020. http://dx.doi.org/10.1007/978-3-030-43085-6_3.

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Soultanas, Panos, and Edward Bolt. "Replicative DNA Helicases and Primases." In Molecular Life Sciences, 1–9. New York, NY: Springer New York, 2014. http://dx.doi.org/10.1007/978-1-4614-6436-5_57-6.

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Soultanas, Panos, and Edward Bolt. "Replicative DNA Helicases and Primases." In Molecular Life Sciences, 1062–69. New York, NY: Springer New York, 2018. http://dx.doi.org/10.1007/978-1-4614-1531-2_57.

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Yamakawa, Emeritus Hiromi. "Applications to Circular DNA." In Helical Wormlike Chains in Polymer Solutions, 225–60. Berlin, Heidelberg: Springer Berlin Heidelberg, 1997. http://dx.doi.org/10.1007/978-3-642-60817-9_7.

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Тези доповідей конференцій з теми "DnaB helicase"

Ha, T., H. P. Babcock, W. Cheng, T. M. Lohman, and S. Chu. "Single molecule fluorescence study of DNA helicase activity." In Conference on Lasers and Electro-Optics (CLEO 2000). Technical Digest. Postconference Edition. TOPS Vol.39. IEEE, 2000. http://dx.doi.org/10.1109/cleo.2000.907430.

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Zhou, Lifeng, Alexander E. Marras, Carlos E. Castro, and Hai-jun Su. "Pseudo-Rigid-Body Models of Compliant DNA Origami Mechanisms." In ASME 2015 International Design Engineering Technical Conferences and Computers and Information in Engineering Conference. American Society of Mechanical Engineers, 2015. http://dx.doi.org/10.1115/detc2015-46838.

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In this paper, we introduce the strategy of designing and analyzing compliant nanomechanisms fabricated with DNA origami which we call compliant DNA origami mechanism (CDOM). The rigid, compliant and flexible parts are constructed by a bunch of double-stranded DNA (dsDNA) helices, fewer dsDNA helices and single-stranded DNA (ssDNA) strands respectively. Just like in macroscopic compliant mechanisms, a CDOM generates its motion via deformation of at least one structural member. During the motion, strain energy is stored and released in the mechanism. These CDOM can suppress thermal fluctuations due to the internal mechanical energy barrier for motion. An example of compliant hinge joint and a bistable four-bar CDOM fabricated with DNA origami are discussed at the end of this paper. The classic pseudo-rigid-body (PRB) model for compliant mechanism is successfully employed to the analysis of these DNA origami nanomechanisms. This PRB model has been used to guide the design of a bistable CDOM for a desired energy landscape.

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Lee, C. H., H. Teng, and J. S. Chen. "Atomistic to Continuum Modeling of DNA Molecules." In ASME 2010 First Global Congress on NanoEngineering for Medicine and Biology. ASMEDC, 2010. http://dx.doi.org/10.1115/nemb2010-13157.

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The mechanical properties of DNA has very important biological implication. For example, the bending and twisting rigidities of DNA affect how it wraps around histones to form chromosomes, bends upon interactions with proteins, supercoils during replication process, and packs into the confined space within a virus. Many biologically important processes involving DNA are accompanied by the deformations of double helical structure of DNA.

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Laughton, C. A., and S. Neidle. "DNA Triple Helices a Molecular Dynamics Study." In Advances in biomolecular simulations. AIP, 1991. http://dx.doi.org/10.1063/1.41360.

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Afifi, Marwa, Breelyn A. Wilky, Catherine Kim, Venu Raman, and David Loeb. "Abstract 4170: The RNA helicase, DDX3, modulates DNA damage repair in Ewing sarcoma." In Proceedings: AACR Annual Meeting 2018; April 14-18, 2018; Chicago, IL. American Association for Cancer Research, 2018. http://dx.doi.org/10.1158/1538-7445.am2018-4170.

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Vanhauwaert, Suzanne, Kaat Durinck, Els Janssens, Givani Dewyn, Bram De Wilde, Genevieve Laureys, Daniel Carter, et al. "Abstract 4886: The BRIP1 DNA helicase is a 17q dosage sensitive cooperative driver in neuroblastoma." In Proceedings: AACR Annual Meeting 2017; April 1-5, 2017; Washington, DC. American Association for Cancer Research, 2017. http://dx.doi.org/10.1158/1538-7445.am2017-4886.

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Manoj, P., Chang-Ki Min, Taiha Joo, and C. T. Aravindakumar. "Ultrafast Charge Transfer Dynamics of a Modified Double Helical DNA." In International Conference on Ultrafast Phenomena. Washington, D.C.: OSA, 2006. http://dx.doi.org/10.1364/up.2006.thd6.

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Zoppoli, Gabriele, Marie Regairaz, Elisabetta Leo, William C. Reinhold, and Yves Pommier. "Abstract 4693: The putative DNA/RNA Helicase Schlafen-11 sensitizes cancer cells to topoisomerase I inhibitors." In Proceedings: AACR 103rd Annual Meeting 2012‐‐ Mar 31‐Apr 4, 2012; Chicago, IL. American Association for Cancer Research, 2012. http://dx.doi.org/10.1158/1538-7445.am2012-4693.

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Baumstark, Daniela, Sina Berndl, Clemens Wagner, Elke Mayer-Enthart, Janez Barbaric, and Hans-Achim Wagenknecht. "Fluorescent and self-assembled helical chromophore arrays based on DNA architecture." In XIVth Symposium on Chemistry of Nucleic Acid Components. Prague: Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, 2008. http://dx.doi.org/10.1135/css200810286.

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Hussain Shah, Syed Imran, Saptarshi Ghosh, and Sungjoon Lim. "A Novel DNA Inspired Mode and Frequency Reconfigurable Origami Helical Antenna." In 2018 IEEE International Symposium on Antennas and Propagation & USNC/URSI National Radio Science Meeting. IEEE, 2018. http://dx.doi.org/10.1109/apusncursinrsm.2018.8608572.

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Звіти організацій з теми "DnaB helicase"

Bussen, Wendy L. The Roles of the BLM Helicase in Homologous Recombination and DNA Repair. Fort Belvoir, VA: Defense Technical Information Center, May 2005. http://dx.doi.org/10.21236/ada436923.

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Beal, P. A., and P. B. Dervan. Recognition of Double Helical DNA by Alternate Strand Triple Helix Formation. Fort Belvoir, VA: Defense Technical Information Center, June 1992. http://dx.doi.org/10.21236/ada251499.

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Elbaum, Michael, and Peter J. Christie. Type IV Secretion System of Agrobacterium tumefaciens: Components and Structures. United States Department of Agriculture, March 2013. http://dx.doi.org/10.32747/2013.7699848.bard.

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Objectives: The overall goal of the project was to build an ultrastructural model of the Agrobacterium tumefaciens type IV secretion system (T4SS) based on electron microscopy, genetics, and immunolocalization of its components. There were four original aims: Aim 1: Define the contributions of contact-dependent and -independent plant signals to formation of novel morphological changes at the A. tumefaciens polar membrane. Aim 2: Genetic basis for morphological changes at the A. tumefaciens polar membrane. Aim 3: Immuno-localization of VirB proteins Aim 4: Structural definition of the substrate translocation route. There were no major revisions to the aims, and the work focused on the above questions. Background: Agrobacterium presents a unique example of inter-kingdom gene transfer. The process involves cell to cell transfer of both protein and DNA substrates via a contact-dependent mechanism akin to bacterial conjugation. Transfer is mediated by a T4SS. Intensive study of the Agrobacterium T4SS has made it an archetypal model for the genetics and biochemistry. The channel is assembled from eleven protein components encoded on the B operon in the virulence region of the tumor-inducing plasmid, plus an additional coupling protein, VirD4. During the course of our project two structural studies were published presenting X-ray crystallography and three-dimensional reconstruction from electron microscopy of a core complex of the channel assembled in vitro from homologous proteins of E. coli, representing VirB7, VirB9, and VirB10. Another study was published claiming that the secretion channels in Agrobacterium appear on helical arrays around the membrane perimeter and along the entire length of the bacterium. Helical arrangements in bacterial membranes have since fallen from favor however, and that finding was partially retracted in a second publication. Overall, the localization of the T4SS within the bacterial membranes remains enigmatic in the literature, and we believe that our results from this project make a significant advance. Summary of achievements : We found that polar inflations and other membrane disturbances relate to the activation conditions rather than to virulence protein expression. Activation requires low pH and nutrient-poor medium. These stress conditions are also reflected in DNA condensation to varying degrees. Nonetheless, they must be considered in modeling the T4SS as they represent the relevant conditions for its expression and activity. We identified the T4SS core component VirB7 at native expression levels using state of the art super-resolution light microscopy. This marker of the secretion system was found almost exclusively at the cell poles, and typically one pole. Immuno-electron microscopy identified the protein at the inner membrane, rather than at bridges across the inner and outer membranes. This suggests a rare or transient assembly of the secretion-competent channel, or alternatively a two-step secretion involving an intermediate step in the periplasmic space. We followed the expression of the major secreted effector, VirE2. This is a single-stranded DNA binding protein that forms a capsid around the transferred oligonucleotide, adapting the bacterial conjugation to the eukaryotic host. We found that over-expressed VirE2 forms filamentous complexes in the bacterial cytoplasm that could be observed both by conventional fluorescence microscopy and by correlative electron cryo-tomography. Using a non-retentive mutant we observed secretion of VirE2 from bacterial poles. We labeled the secreted substrates in vivo in order detect their secretion and appearance in the plant cells. However the low transfer efficiency and significant background signal have so far hampered this approach.

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